Bioinformatics has evolved as a great tool for molecular biologists. There are various tools available for helping in reducing the time required to analyze biological materials be it DNA, RNA, Proteins etc. I wish to list here few of the commonly used tools. Please send me suggestions to improve the content. If you like or dislike something, let me know, your inputs matters. contact me: drsanjivk[at]gmail[dot]com

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Wednesday, April 30, 2014

Functional Annotation of Hypothetical proteins

Experimental work is though time
taking but direct approach for functional annotation of hypothetical proteins;
however, at times it is difficult to decide upon the experimental design for a
relatively new class of a protein. With increasing size and quality of various
protein databases, it is becoming relatively easier to look for the
experimental design for the probable function of a protein. Following are the
steps that can be used in choosing the type of experimental analysis that needs
to be performed and the substrate to be used during laboratory tests.

1.If
the protein is predicted to be an enzyme, BLAST results normally
indicates its closely related proteins that can be looked upon for the
experimental procedures to be performed as indicated by the matching hits (look
for the papers on those proteins that might indicate the type of related
function the protein might perform).

2.With
the increasing domain databases, it is possible to analyze the protein domain
wise indicating the ability to perform certain kind of biochemical reactions if
any. The NCBI’s Conserved
Doamin Database (CDD), Pfam and InterProScan databases have a large
number of conserved domains that defines a functional class. Presence of
certain domain is also indicative of the possible activity of the protein and
therefore the type of substrate to be used for defining its chemical activity
in laboratory could be helpful.

3.Composition based analysis of protein: there are various bioinformatics
tools available online to studying the amino acid composition based analysis of
protein informing various properties which help in indicating the properties of
protein which later help with the functional annotation of the proteins i.e. Protparam, SPAAN, MP3 and a lot more etc.

4.Homology based modeling: this is an important step in
determining the functional annotation of protein based on the structure of the
protein, though it may be difficult for the proteins with low identity
(<30%) with the already known crystal structures of the protein. However, a
good homology model can be an important step towards determining functional
annotation for a protein. So also the secondary and tertiary structure
prediction of the protein will tell the similar functional categories thereby
help in designing relative experimental assays. Some of the commonly used
homology based modeling tools are listed here http://bioinformatictools.blogspot.in/2012/01/homology-modeling-of-proteins.html.

5.Phylogenetic analysis: Phylogenetic analysis not only shows
evolutionary divergence of the protein but also act as an important step
towards functional conservation of the protein. This helps in determining the
degree of functional similarity with other related homologous proteins. Thus,
determining the appropriate experimental assays towards functional annotation
of the protein. With the help of molecular dynamic simulation, this also helps
in-silico assessment of the ability of substrate to bind to the protein. In
fact it can cut down from large number of substrate molecules to the top most
hits, helping to prioritize the experimental analysis, saving time and
resources.

6.It
is sometimes a bit difficult while working with novel proteins for which
relevant data is almost negligible worldwide, so you can wait till you get more
information.